- wasAtReceiverRootLevel() - Method in exception info.bioinfweb.jphyloio.exception.IllegalEventException
-
- wasDelimited() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
-
- wasValueDelimited() - Method in class info.bioinfweb.jphyloio.formats.text.KeyValueInformation
-
Determines whether the read value was delimited in the source stream.
- WORD_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
-
- write() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter
-
Writes the tree data specified in the constructor to the specified stream.
- write() - Method in class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
-
- writeAttribute(String, String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeAttribute(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeAttribute(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeBlockEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeBlockEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
-
- writeBlockStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeBlockStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
-
- writeCData(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeCharacters(char[], int, int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeCharacters(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeCharSequencePartContent(JPhyloIOEventReceiver, long, long, CharSequence) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeCommandEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeCommandEnd() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
-
- writeComment(BasicEventReceiver<?>, CommentEvent, String, String) - Static method in class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver
-
- writeComment(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeComments() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
-
- writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
-
Always throws an IllegalArgumentException, since this default implementation does not contain
any objects.
- writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
-
- writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
-
- writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
-
- writeContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String) - Method in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter
-
Writes the nested events in the specified object describing its contents.
- writeCustomXML(XMLStreamWriter, ReadWriteParameterMap, XMLEvent) - Static method in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
-
- writeCustomXMLTag(XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
-
- writeDefaultNamespace(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeDocument(DocumentDataAdapter, File, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
-
- writeDocument(DocumentDataAdapter, OutputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
-
- writeDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
-
- writeDocument(DocumentDataAdapter, OutputStream, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
-
Writes the data provided by the data adapter to a document in the according format of the implementing class.
- writeDocument(DocumentDataAdapter, File, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
-
Writes the data provided by the data adapter to a document in the according format of the implementing class.
- writeDocument(DocumentDataAdapter, Writer, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventWriter
-
Writes the data provided by the data adapter to a document in the according format of the implementing class.
- writeDTD(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeElementReference(SetElementEvent) - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
-
- writeEmptyElement(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
It depends on the implementation of XMLStreamWriter returned by XMLOutputFactory.createXMLStreamWriter(java.io.Writer)
if a self-closing tag or a separate start and end tag is written by this method.
- writeEmptyElement(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
It depends on the implementation of XMLStreamWriter returned by XMLOutputFactory.createXMLStreamWriter(java.io.Writer)
if a self-closing tag or a separate start and end tag is written by this method.
- writeEmptyElement(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
It depends on the implementation of XMLStreamWriter returned by XMLOutputFactory.createXMLStreamWriter(java.io.Writer)
if a self-closing tag or a separate start and end tag is written by this method.
- writeEndDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeEndElement() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeEntityRef(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeKeyValueExpression(Writer, String, String) - Static method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeLabeledIDAttributes(LabeledIDEvent) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
-
- writeLabeledIDAttributes(LabeledIDEvent, String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
-
- writeLineBreak(Writer, ReadWriteParameterMap) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
-
Writes the line separator, as it is specified in the parameter map or the line separator
of the current operating system, if the map contains no according entry.
- writeLineStart(Writer, String) - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
-
- writeLineStart(Writer, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeLineStart(String) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
-
- writeLinkCommand(String, String, EventContentType) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
-
- writeLinkCommand(String, String, EventContentType) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusWriterStreamDataProvider
-
- writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent, QName, boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
-
- writeListSequencePartContent(JPhyloIOEventReceiver, long, long, List<?>) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in interface info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter
-
Writes events describing the metadata associated with the object represented by this instance.
- writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter
-
This default implementation does nothing and can be overwritten by inherited classes if necessary.
- writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter
-
- writeMetadata(ReadWriteParameterMap, JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.UndefinedOTUListDataAdapter
-
- writeMetadata() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
-
Write the metadata stored in this receiver into a Newick/Nexus hot comment.
- writeNamespace(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeProcessingInstruction(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeProcessingInstruction(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writePropertyTag(URIOrStringIdentifier, URIOrStringIdentifier, String, boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver
-
- writeRemainingStandardTokenDefinitions() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLTokenSetEventReceiver
-
- WriterStreamDataProvider<R extends AbstractEventWriter<? extends WriterStreamDataProvider<R>>> - Class in info.bioinfweb.jphyloio
-
- WriterStreamDataProvider(R) - Constructor for class info.bioinfweb.jphyloio.WriterStreamDataProvider
-
- writeSequencePartContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String, long, long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
-
- writeSequencePartContentData(ReadWriteParameterMap, JPhyloIOEventReceiver, String, long, long) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
-
Implementing classes must write a sequence of events here, that describe the sequence tokens present in
the specified column range.
- writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URIOrStringIdentifier, Object, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
Writes an event subsequence modeling a literal metadata annotation with a simple value.
- writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, QName, QName, Object, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
Writes an event subsequence modeling a literal metadata annotation with a simple value.
- writeSimpleLiteralMetadata(JPhyloIOEventReceiver, String, String, QName, QName, Object) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
Writes an event subsequence modeling a literal metadata annotation with a simple value.
- writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
-
Implementations of this method should write a single matrix to their target format.
- writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
-
- writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator<String>, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
-
- writeStartDocument() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeStartDocument(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeStartDocument(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeStartElement(String, String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeStartElement(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeStartElement(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
-
- writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URI, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, URIOrStringIdentifier, URI) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, QName, URI, String) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeTerminalResourceMetadata(JPhyloIOEventReceiver, String, String, QName, URI) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOWritingUtils
-
- writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator
-
- writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator
-
Writes the string representation of the specified object to an XML stream.
- writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider<?>) - Method in interface info.bioinfweb.jphyloio.objecttranslation.ObjectTranslator
-
Writes the XML representation of the specified object into the specified XML writer.
